Korean Journal of Environmental Biology (환경생물)

Korean Society of Environmental Biology (한국환경생물학회)
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Analysis of Bacterial Community Structure in Gossi Cave by Denaturing Gradient Gel Electrophoresis (DGGE)

DGGE를 이용한 동굴 생태계 세균 군집 구조 분석

  • Published : 2004.03.01
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Abstract

The bacterial community of water stream, soil and guano in Gossi cave was examined by using PCR amplified the 16S rDNA-denaturing gradient gel electrophoyesis (DGGE). In this study, the genetic diversity and the similarity of bacterial community between open area and non - open area toy cave tour were investigated, and the seasonable variation pattern was compared each other. DGGE is attractive technique, as it sepayate same length dsDNA according to sequence variation typical 16S rDNA genes. The diversity and similarity of bacterial community in cave was analyzed by GC341f and PRUN518r primer sets foy amplification of V3 region of eubacteria 16S rDNA. The specific DGGE band profile of the cave water gives the possibility that the specific bacterial cell can be adapting to the specific cave environment and living in the cave. The DGGE band profiles of all samples with guano were compared and analyzed by image analyzer, in which mutual band profile was compared to be and the band intensity of guano was the highest. From these result, it is thought that the guano was main nutrient source and influenced on the community structure of the cave environment where is nutritionally limited. Pseudomonas sp. NZ060, Pseudomonas pseudoalcaligenes, uncultured Variovorax sp. and soli bacterium NS7 were identified to be on some sample from analysing DNA sequence of some DGGE band.

동굴 내 정점별 세균 군집 구조를 분석하기 위하여 PCf amplified 16S rDNA denaturing gradient gel electrophoresis(DGGE)를 적용하였다. DGGE는 동일한 분자량을 갖는 dsDNA band라고 할지라도, 각각의 염기서열 차이에 따라 전기영동 상에서 고유한 band양상을 나타낼 수 있다. eubacteria의 16S rDNA V3region을 증폭하기 위해 GC341F와 PRUN518r을 primer로 사용하여 지하수내에 미생물 군집의 다양성과 유사성을 분석하였다. DGGE band 양상을 통해 동굴내의 세균 군집 구조는 외부 환경에 비해 상대적으로 종다양성이 낮으며 동굴내 에서 특이적으로 서식하는 종이 있음을 확인하였다. 또한 유기 영양물질의 공급이 제한되어 있는 동굴에서 구아노가 주요 유기 영양물질의 공급원으로서 큰 영향을 미치고 있는 것으로 파악되었다. DGGE 상의 일부 band의 염기서열분석 결과 Pseudomonas sp. NZ060과 Pseudomonas pseudoalcaligenes, uncultured Variovorax sp., soil bacterium NS7로 동정되었다.

Keywords

References

  1. 한국식물보호학회지 v.19 no.2 한국산 동굴 거미의 연구 1. 남궁준
  2. 강원도의 자연동굴과 동물상. 강원도의 희귀자원 조사보고서 남궁준
  3. 성류동굴 종합학술보고서 민경희
  4. 고수동굴 보존대책조사연구보고서 민경희
  5. 영월 고씨동굴 종합학술조사보고서 우경식
  6. 성류동굴의 천연기념물 지정을 위한 기초조사 최기철;남궁준
  7. Microbiol. Rev. v.59 Phylogenic identification and in situ detection of individual microbial cells without cultivation Aman,R.I.;W.Ludwing;K.H.Schleifer
  8. Geomicrobiol. J. v.7 Numbers, diversity, and morphological characteristics of aerobic, chemoheterotrophic bacteria in deep subsurface sediments from a site in South Carolina Balkwill,D.L. https://doi.org/10.1080/01490458909377848
  9. 1993 International Symposium on Subsurface Microbiology B-32 Esimates of intact but nonviable and viable but nonculturable microorganism in subsurface sediments from six boreholes located in wet and dry climatic regions of the United States Brockman,F.J.;D.B.Ringelberg;D.C.White;J.K.Fredrickson;D.L.Balkwill;T.L.Kieft;T.J.Phelps;W.C.Ghiorse
  10. Microb. Ecol. v.36 Spatial homogeneity of abundant bacterial 16S rRNA molecules in grassland soils Felske,A.;A.D.L.Akkermans https://doi.org/10.1007/s002489900090
  11. Appl. Environ. Microbiol. v.61 Aromatic-degrading Sphongomonas isolates from the deep subsurface Fredrickson,J.K.;D.L.Balkwill;G.R.Drake;M.F.Romine;D.B.Ringelberg;D.C.White
  12. Appl. Environ. Microbiol. v.65 Molecular analysis of the methane-oxidizing microbial community in rice field soil by targeting the genes of the 16S rRNA, particulate methane monooxygenase, and methanol dehydrogenase Henckel,T.;M.Friedrich;R.Conrad
  13. Appl. Environ. Microbiol. v.33 Use of nuclepore filters for counting bacteria by fluorescence microscopy Hobbie,J.E.;R.J.Daley;S.Jasper
  14. Appl. Environ. Microbiol. v.62 DNA recovery from soils of diverse composition Jizhong,Z.;M.A.Brus;J.M.Tiedje
  15. Cave v.8 no.9 A Investigation of counter-measure about corruption and pollution in Go-Soo Cave Lee;Park;No;Hong
  16. Appl. Environ. Microbiol. v.59 Profiling of complex microbial populations using denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified gene coding for 16S rRNA Muyzer,G.;E.C. de Waal;A.Uitterlinden
  17. Proc. Natl. Acad. Sci. v.76 Mathematics model for studying genetic variation in terms of restriction endonuclease Nei,M.;W.H.Li https://doi.org/10.1073/pnas.76.10.5269
  18. Appl. Environ. Microbiol. v.63 Distribution of bacterioplankton in meromictic lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments codin for 16S rRNA OvreAs,L.;L.Forney;F.L.Daae;V.Torsvik
  19. FEMS Microbiol. Ecol. v.19 16S rRNA gene diversity of attached and unattached bacteria in boreholes along the access tunnel to the Åsp$\"{o}$ hard rock laboratory Pedersen,K.;J.Arlinger;S.Ekendahl;L.Halbeck
  20. Mol. Ecol. v.5 Diversity and distribution of subterranean bacteria in groundwater at Oklo in Gabon, Africa, as determined by 16S rRNA gene sequencing Pedersen,K.;J.Arlinger;L.Hallbeck;C.Pettersson https://doi.org/10.1111/j.1365-294X.1996.tb00332.x
  21. Numerical taxonomy The principles and practice of numerical classfication Sneath,P.H.;R.R.Sokal
  22. Appl. Environ. Microbiol. v.55 Simple, rapid method for direct isolation of nucleic accids from aquatic environments Somerville,H.C.;I.T.Knight;W.L.Straube;R.R.Colwell
  23. The biology of caverniculous animals Vandel,A.
  24. Appl. Environ. Microbiol. v.63 Characterization of Thiobaccillus thioparus LV43 and Its distribution in a chemoautotrophically based groundwater ecosystem Vlasceanu,I.;R.Pora;B.K.Kinkle
  25. Appl. Environ. Microbiol. v.65 Methanotroph diversity in landfill soil: isolation of novel type Ⅰ and type Ⅱ methanotrophs whose presence was suggested by culture-independent 16S ribosomal DNA analysis Wise,M.G.;J.V.McArthur;L.J.Shimkets